Multiple platform build/check report for BioC 3.21 - BUILD results for wppi on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
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 kunpeng2

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: 1.16.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2025-09-23 06:31:30 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 06:42:08 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 638.2 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
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###
### 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
[2025-09-23 06:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-22
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-22 20:19:58 UTC; unix
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-09-23 06:31:53] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-23; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-23 06:31:54] [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=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; 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=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-09-23 06:31:54] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-09-22); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 1.16.0(2025-09-22); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-09-23 06:31:54] [INFO]    [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; 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
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:54] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-09-23 06:31:55] [INFO]    [wppi] Executing WPPI workflow.
[2025-09-23 06:31:55] [INFO]    [wppi] Collecting database knowledge.
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-09-23 06:31:55] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:31:55] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-09-23 06:31:55] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-09-23 06:31:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-09-23 06:31:55] [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=TRUE,ssl_verifyhost=TRUE]
[2025-09-23 06:31:56] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-09-23 06:31:56] [TRACE]   [OmnipathR] Downloaded 16 Kb in 1.454833s from purl.obolibrary.org (11 Kb/s); Redirect: 1.212332s, DNS look up: 0.054986s, Connection: 0.06128s, Pretransfer: 0.087168s, First byte at: 1.451805s
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[2025-09-23 06:32:24] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-09-23 06:32:24] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-09-23 06:32:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:32:24] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-09-23 06:32:24] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 391404 records
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-09-23 06:32:25] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:32:25] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-09-23 06:32:25] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-09-23 06:32:25] [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=TRUE,ssl_verifyhost=TRUE]
[2025-09-23 06:32:25] [TRACE]   [OmnipathR] `gz` compressed file, downloading to temporary location: `/home/biocbuild/tmp/RtmpbDGyoF/goa_human.gaf.gz`
[2025-09-23 06:32:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-09-23 06:32:35] [TRACE]   [OmnipathR] Downloaded 14.7 Mb in 10.555938s from current.geneontology.org (1.4 Mb/s); Redirect: 0s, DNS look up: 0.299841s, Connection: 0.437384s, Pretransfer: 0.437441s, First byte at: 0.594311s
[2025-09-23 06:32:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Content-Type: application/gzip; Content-Length: 15420674; Connection: keep-alive; Date: Tue, 23 Sep 2025 04:11:06 GMT; 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"; ETag: "4750fafbd9497117ae5ff560a23098cd-2"; Server: AmazonS3; X-Cache: Hit from cloudfront; Via: 1.1 1687ffc8e5ebfcbf00ea62e744809ee8.cloudfront.net (CloudFront); X-Amz-Cf-Pop: MRS53-P1; X-Amz-Cf-Id: Da9r5fikaQC_iapFpo8JNnil2k4w9V996yZF62vA7xyOQPexaqmT9g==; Age: 8868
[2025-09-23 06:32:50] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-09-23 06:32:50] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-09-23 06:32:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:32:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:32:50] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-09-23 06:32:51] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 993392 records
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-09-23 06:32:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:32:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-23 06:32:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-09-23 06:32:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-23 06:32:51] [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=TRUE,ssl_verifyhost=TRUE]
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-23 06:32:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-23 06:35:54] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 Not Found.
[2025-09-23 06:35:59] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-23 06:35:59] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-23 06:35:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-23 06:35:59] [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=TRUE,ssl_verifyhost=TRUE]
[2025-09-23 06:35:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-23 06:35:59] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-23 06:39:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 Not Found.
[2025-09-23 06:39:05] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-23 06:39:05] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-23 06:39:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-23 06:39:05] [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=TRUE,ssl_verifyhost=TRUE]
[2025-09-23 06:39:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-09-23 06:39:05] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-23 06:42:07] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 Not Found.
[2025-09-23 06:42:07] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-23 06:42:07] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-22
[2025-09-23 06:42:07] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-22 20:19:58 UTC; unix
[2025-09-23 06:42:07] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-09-23 06:42:07] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-09-23 06:42:07] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-23; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-23 06:42:07] [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=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; 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=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-09-23 06:42:08] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-09-22); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-09-22); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-09-23 06:42:08] [INFO]    [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; 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]
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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