Multiple platform build/check report for BioC 3.22 - BUILD results for wppi on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4832
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4620
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4565
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4563
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*
BUILD results for wppi on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.
raw results
Summary

Package: wppi
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2025-09-26 04:16:24 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 04:27:00 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 636.1 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2025-09-26 04:16:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-25 20:20:06 UTC; unix
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-26 04:16:46] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-26; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-26 04:16:46] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-26 04:16:47] [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); 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 0.6.37(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 1.1.3(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 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); 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 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-25); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); 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 2.4.3(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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-09-25); 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)
[2025-09-26 04:16:47] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-09-26 04:16:47] [INFO]    [wppi] Executing WPPI workflow.
[2025-09-26 04:16:47] [INFO]    [wppi] Collecting database knowledge.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-09-26 04:16:47] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:16:47] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-09-26 04:16:47] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-09-26 04:16:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-09-26 04:16:49] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-09-26 04:16:49] [TRACE]   [OmnipathR] Downloaded 16 Kb in 1.529494s from purl.obolibrary.org (10.5 Kb/s); Redirect: 1.285192s, DNS look up: 0.056604s, Connection: 0.063847s, Pretransfer: 0.089305s, First byte at: 1.528925s
[2025-09-26 04:16:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Fri, 26 Sep 2025 04:21:13 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; CF-RAY: 984ff9235f6dfd91-SIN; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; cf-cache-status: DYNAMIC; Set-Cookie: __cf_bm=.nEVQGEra3s0FQEQIIZ6eLhb1c0er20NxWhwYi0aozY-1758860473-1.0.1.1-RoonM7bx0Iw4H.6o_RqfyelKjxH9J5aa7NZlBpUWSI.fd70qasNO5h6erQJ16rpuYC.wKIUsdGckW2EBHBwSiETofkPrhU_IoA6Y1jCGxQM; path=/; expires=Fri, 26-Sep-25 04:51:13 GMT; domain=.obolibrary.org; HttpOnly; Server: cloudflare; HTTP/2 302 ; date: Fri, 26 Sep 2025 04:21:13 GMT; content-type: text/html; charset=utf-8; content-length: 0; vary: X-PJAX, X-PJAX-Container, Turbo-Visit, Turbo-Frame, X-Requested-With,Accept-Encoding, Accept, X-Requested-With; location: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-09-01/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; 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=%2FxPwIt51mb5OX5xBYawp%2BdDCOzDAeVjmsM0emE%2BpdmcLz3nk7nKG78NNQJ93Tbvpj3mC4usNJ%2FB5QdKrrpWht%2FoOgVwURay6X%2BbgYuifZFP36jWrUun%2FOMnhAWasjFXRxCwzzxhUSwkUQH7FK7Htgt45hsBnD0O0mlhDUN%2BF0iFFCt%2B9S8DPWhKkQGYnXqNB4e6AwHtYXQf%2BweBTBifkxhsDJRnCy%2FtRcJFbDcLqYwBvdjfX6kqF%2B03xJjzTxPvOXyPq6J5l%2FIHpoEAcXJE%2FtQ%3D%3D--kzoOtDE6Myj%2BHgkP--063l2ds2oQ4CGnFctAndug%3D%3D; Path=/; HttpOnly; Secure; SameSite=Lax; set-cookie: _octo=GH1.1.1995389748.1758860473; Path=/; Domain=github.com; Expires=Sat, 26 Sep 2026 04:21:13 GMT; Secure; SameSite=Lax; set-cookie: logged_in=no; Path=/; Domain=github.com; Expires=Sat, 26 Sep 2026 04:21:13 GMT; HttpOnly; Secure; SameSite=Lax; x-github-request-id: E1BA:1A0418:29B0D5:2E6495:68D614B9; HTTP/2 302 ; date: Fri, 26 Sep 2025 04:21:13 GMT; content-type: text/html; charset=utf-8; content-length: 0; vary: X-PJAX, X-PJAX-Container, Turbo-Visit, Turbo-Frame, X-Requested-With,Accept-Encoding, Accept, X-Requested-With; location: https://release-assets.githubusercontent.com/github-production-release-asset/41063438/f053b339-a907-4c25-9873-0786f93e8499?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-09-26T05%3A21%3A02Z&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=2025-09-26T04%3A20%3A26Z&ske=2025-09-26T05%3A21%3A02Z&sks=b&skv=2018-11-09&sig=93Rtvwbl%2F7KgGEl%2Bexjk7G6u%2F3szjgMX5%2BY3st%2B7UP4%3D&jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmVsZWFzZS1hc3NldHMuZ2l0aHVidXNlcmNvbnRlbnQuY29tIiwia2V5Ijoia2V5MSIsImV4cCI6MTc1ODg2MDc3MywibmJmIjoxNzU4ODYwNDczLCJwYXRoIjoicmVsZWFzZWFzc2V0cHJvZHVjdGlvbi5ibG9iLmNvcmUud2luZG93cy5uZXQifQ.POaIrabd63S-3Cpi81698Jhi2sd2ZrcgiEnVrlBvYAc&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; 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: E1BA:1A0418:29B11C:2E64F3:68D614B9; HTTP/2 200 ; last-modified: Tue, 02 Sep 2025 16:35:47 GMT; etag: "0x8DDEA3EC58CBCFE"; server: Windows-Azure-Blob/1.0 Microsoft-HTTPAPI/2.0; x-ms-request-id: ea394b0c-001e-0015-5e58-2ef6e6000000; x-ms-version: 2018-11-09; x-ms-creation-time: Tue, 02 Sep 2025 16:35:47 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: 0; date: Fri, 26 Sep 2025 04:21:14 GMT; x-served-by: cache-iad-kcgs7200129-IAD, cache-qpg120111-QPG; x-cache: HIT, MISS; x-cache-hits: 13, 0; x-timer: S1758860474.091396,VS0,VE231; content-disposition: attachment; filename=genes_to_phenotype.txt; content-type: application/octet-stream; content-length: 24100644
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-09-26 04:17:14] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:17:14] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-09-26 04:17:14] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 391404 records
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-09-26 04:17:14] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:17:14] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-09-26 04:17:14] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-09-26 04:17:14] [TRACE]   [OmnipathR] `gz` compressed file, downloading to temporary location: `/home/biocbuild/tmp/RtmpGSaJab/goa_human.gaf.gz`
[2025-09-26 04:17:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-09-26 04:17:27] [TRACE]   [OmnipathR] Downloaded 14.7 Mb in 12.975796s from current.geneontology.org (1.1 Mb/s); Redirect: 0s, DNS look up: 0.569859s, Connection: 0.707418s, Pretransfer: 0.707482s, First byte at: 0.865229s
[2025-09-26 04:17:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Content-Type: application/gzip; Content-Length: 15420674; Connection: keep-alive; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 379; Last-Modified: Fri, 25 Jul 2025 22:43:54 GMT; x-amz-expiration: expiry-date="Sun, 26 Jul 2026 00:00:00 GMT", rule-id="365days-rule"; Server: AmazonS3; Date: Fri, 26 Sep 2025 04:21:40 GMT; ETag: "4750fafbd9497117ae5ff560a23098cd-2"; X-Cache: Hit from cloudfront; Via: 1.1 bef918445c49bf6d036d07d855e42cd8.cloudfront.net (CloudFront); X-Amz-Cf-Pop: MRS53-P1; X-Amz-Cf-Id: HYuNZOUIlcVNtsZwu69MafJENeanmfiZaY_1cBUPHZLEvf6f9JElLw==; Age: 77875
[2025-09-26 04:17:40] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-09-26 04:17:40] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-09-26 04:17:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:17:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:17:40] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-09-26 04:17:41] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 993392 records
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-09-26 04:17:41] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:17:41] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 04:17:41] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-09-26 04:17:41] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-26 04:17:41] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-26 04:20:44] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 Not Found.
[2025-09-26 04:20:49] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-26 04:20:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-26 04:20:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-26 04:20:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-09-26 04:20:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-26 04:20:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-26 04:23:52] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 Not Found.
[2025-09-26 04:23:57] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-26 04:23:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-26 04:23:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-26 04:23:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-09-26 04:23:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-26 04:23:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-26 04:26:58] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 Not Found.
[2025-09-26 04:26:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-26 04:26:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-26 04:26:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-25 20:20:06 UTC; unix
[2025-09-26 04:26:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-26 04:26:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-26 04:26:59] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-26; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-26 04:26:59] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-26 04:26:59] [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 2.3.3(2025-08-18); 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 0.6.37(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 1.1.3(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 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); 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 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-25); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); 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 2.4.3(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); vroom 1.6.6(2025-09-19); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-09-25); 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)
[2025-09-26 04:26:59] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

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 `req_perform()`:
! HTTP 404 Not Found.
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted