Multiple platform build/check report for BioC 3.22 - BUILD results for wppi on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4670
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4604
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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 kjohnson1

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: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2025-12-09 12:57:00 -0500 (Tue, 09 Dec 2025)
EndedAt: 2025-12-09 12:58:28 -0500 (Tue, 09 Dec 2025)
EllapsedTime: 88.7 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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
[2025-12-09 12:57:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:31] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-09 12:57:31] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-09 12:57:31] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-09 12:57:31] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-08 20:26:03 UTC; unix
[2025-12-09 12:57:31] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-09 12:57:31] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-09 12:57:32] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-09; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-09 12:57:32] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-09 12:57:33] [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 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.18.2(2025-12-08); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(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 1.18.0(2025-12-08); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-09 12:57:33] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:33] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-12-09 12:57:34] [INFO]    [wppi] Executing WPPI workflow.
[2025-12-09 12:57:34] [INFO]    [wppi] Collecting database knowledge.
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-12-09 12:57:34] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:34] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-12-09 12:57:34] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-09 12:57:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-12-09 12:57:34] [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]
[2025-12-09 12:57:35] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-12-09 12:57:35] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.989009s from purl.obolibrary.org (31.6 Kb/s); Redirect: 0.824402s, DNS look up: 0.094644s, Connection: 0.200598s, Pretransfer: 0.310977s, First byte at: 0.982908s
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[2025-12-09 12:57:39] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-12-09 12:57:39] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-12-09 12:57:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:39] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-12-09 12:57:39] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 320212 records
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-12-09 12:57:40] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:57:40] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-12-09 12:57:40] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-12-09 12:57:40] [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]
[2025-12-09 12:57:40] [TRACE]   [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/RtmpuzE3MO/goa_human.gaf.gz`
[2025-12-09 12:57:41] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-12-09 12:57:41] [TRACE]   [OmnipathR] Downloaded 14.8 Mb in 0.489171s from current.geneontology.org (30.3 Mb/s); Redirect: 0.057358s, DNS look up: 0.047459s, Connection: 0.0504s, Pretransfer: 0.068428s, First byte at: 0.207911s
[2025-12-09 12:57:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 301 Moved Permanently; Date: Tue, 09 Dec 2025 17:57:40 GMT; Content-Length: 0; Connection: keep-alive; Location: https://current.geneontology.org/annotations/goa_human.gaf.gz; Vary: accept-encoding; set-cookie: __cf_bm=jGtQJBzZGf_SIBGKpLCXcG6NjJTMDrNWM0olXH3Agr8-1765303060.700832-1.0.1.1-rWtWA1NjwJ_RXfN8kqu4LKq5c66.qPRfRYAIa.aWDbX6qOYFQvelmGFL0X4L6YN2L7y8PT4tuMmXF_D1j5U_HMC36ygFmFHFQATlQkTc1CP00QGhN8DaNTtfni7TMStC; HttpOnly; Path=/; Domain=geneontology.org; Expires=Tue, 09 Dec 2025 18:27:40 GMT; Server: cloudflare; CF-RAY: 9ab662e16bffbdd1-DUB; HTTP/2 200 ; date: Tue, 09 Dec 2025 17:57:40 GMT; content-type: application/gzip; content-length: 15530828; last-modified: Fri, 17 Oct 2025 23:34:40 GMT; x-amz-expiration: expiry-date="Sun, 18 Oct 2026 00:00:00 GMT", rule-id="365days-rule"; etag: "f4bb1e1a606a6604d27f40f3a945907c-2"; x-amz-server-side-encryption: AES256; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 381; accept-ranges: bytes; server: cloudflare; x-cache: Miss from cloudfront; via: 1.1 009b28dd2e1a33c65de17468676b9c46.cloudfront.net (CloudFront); x-amz-cf-pop: CDG50-P4; x-amz-cf-id: k7Zuq9bghn_Qsx2vKZ8gBY1yK8ct4lS125xJGSNFsqKex_x7c6LYPA==; set-cookie: __cf_bm=TzpB3IhUGX6wawT3wnvPE8ihsRdvwtBPZiPG7Xprjww-1765303060.7334535-1.0.1.1-JdjmgR.q32Y62AQW_BzRnKhrvsP5fyLy7GZ5RBaL96slysExHnT0xQZ2W1PxKkSOYKebq32o3.n1JIZuKoiTKm50m9j61bgJjQqZLzAvImxWnYoQSA8ns60S.smY6nQl; HttpOnly; Secure; Path=/; Domain=geneontology.org; Expires=Tue, 09 Dec 2025 18:27:40 GMT; expires: Tue, 09 Dec 2025 21:57:40 GMT; cache-control: public, max-age=14400; cf-cache-status: REVALIDATED; vary: accept-encoding; cf-ray: 9ab662e19ded1b96-DUB
[2025-12-09 12:58:00] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-12-09 12:58:00] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-12-09 12:58:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:58:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:58:00] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-12-09 12:58:02] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 972437 records
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-12-09 12:58:02] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:58:02] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:58:02] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-12-09 12:58:02] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:02] [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]
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:02] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-09 12:58:02] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-09 12:58:07] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:07] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-09 12:58:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:07] [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]
[2025-12-09 12:58:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:07] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-09 12:58:07] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-09 12:58:12] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:12] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-09 12:58:12] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:12] [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]
[2025-12-09 12:58:12] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:12] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-09 12:58:12] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-09 12:58:12] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-09 12:58:12] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-09 12:58:12] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-08 20:26:03 UTC; unix
[2025-12-09 12:58:12] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-09 12:58:12] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-09 12:58:13] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-09; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-09 12:58:13] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-09 12:58:13] [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 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.18.2(2025-12-08); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(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 1.6.7(2025-11-28); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.18.0(2025-12-08); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-09 12:58:13] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-09 12:58:14] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-09 12:58:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-09 12:58:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-09 12:58:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-08 20:26:03 UTC; unix
[2025-12-09 12:58:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-09 12:58:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-09 12:58:15] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-09; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-09 12:58:15] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-09 12:58:15] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(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 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.18.2(2025-12-08); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(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 1.6.7(2025-11-28); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.18.0(2025-12-08); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-09 12:58:15] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-09 12:58:15] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-09 12:58:15] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 2.
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-2.html
[2025-12-09 12:58:15] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:15] [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]
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:15] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-09 12:58:15] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-09 12:58:20] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-09 12:58:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:20] [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]
[2025-12-09 12:58:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:21] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-09 12:58:21] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-09 12:58:26] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-09 12:58:26] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-09 12:58:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:26] [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]
[2025-12-09 12:58:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-09 12:58:26] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-09 12:58:26] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-09 12:58:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-09 12:58:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-09 12:58:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-08 20:26:03 UTC; unix
[2025-12-09 12:58:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-09 12:58:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-09 12:58:26] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-09; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-09 12:58:26] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-09 12:58:27] [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 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.18.2(2025-12-08); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(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 1.6.7(2025-11-28); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.18.0(2025-12-08); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-09 12:58:27] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, 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_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘wppi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted