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###
### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
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* 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
[2025-10-01 20:36:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:44] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-01 20:36:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 20:36:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 20:36:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 20:36:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 20:36:44] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 20:36:45] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 20:36:45] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 20:36:45] [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 3.16.2(2025-10-01); 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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-10-01); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-01 20:36:45] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-01 20:36:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-01 20:36:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-01 20:36:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-01 20:36:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:45] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-10-01 20:36:46] [INFO] [wppi] Executing WPPI workflow.
[2025-10-01 20:36:46] [INFO] [wppi] Collecting database knowledge.
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-10-01 20:36:46] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:46] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-10-01 20:36:46] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-10-01 20:36:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-01 20:36:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-01 20:36:46] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-01 20:36:46] [TRACE] [OmnipathR] Downloaded 4 Kb in 0.676167s from purl.obolibrary.org (6 Kb/s); Redirect: 0.563047s, DNS look up: 0.145052s, Connection: 0.191707s, Pretransfer: 0.356588s, First byte at: 0.675252s
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x-cache: HIT; x-cache-hits: 0; x-timer: S1759365407.828662,VS0,VE3; content-disposition: attachment; filename=genes_to_phenotype.txt; content-type: application/octet-stream; content-length: 24100644
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-10-01 20:36:49] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:49] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-10-01 20:36:49] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 391404 records
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-10-01 20:36:49] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:36:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:36:49] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-10-01 20:36:49] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-10-01 20:36:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-01 20:36:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 20:36:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-01 20:36:49] [TRACE] [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/RtmpGrNjYx/goa_human.gaf.gz`
[2025-10-01 20:36:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-01 20:36:50] [TRACE] [OmnipathR] Downloaded 14.7 Mb in 0.785531s from current.geneontology.org (18.7 Mb/s); Redirect: 0s, DNS look up: 0.022626s, Connection: 0.023316s, Pretransfer: 0.023355s, First byte at: 0.642807s
[2025-10-01 20:36:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 379; x-amz-expiration: expiry-date="Sun, 26 Jul 2026 00:00:00 GMT", rule-id="365days-rule"; Server: AmazonS3; ETag: "4750fafbd9497117ae5ff560a23098cd-2"; X-Cache: Hit from cloudfront; X-Amz-Cf-Pop: BOS50-P5; X-Amz-Cf-Id: MjG0H38snx_0LpXM1KyquG8hLNrqcKBn70vMrNi-icFW1Jjx7As95w==; Content-Length: 15420674; Content-Type: application/gzip; Last-Modified: Fri, 25 Jul 2025 22:43:54 GMT; Date: Wed, 01 Oct 2025 09:37:26 GMT; Age: 19669; Via: 1.1 7e0c1ebb759362e1d5ed505d30e7b186.cloudfront.net (CloudFront), 1.1 phswsa5.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2025-10-01 20:37:01] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-10-01 20:37:01] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-10-01 20:37:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:37:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:37:01] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-10-01 20:37:02] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 993392 records
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-10-01 20:37:02] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:37:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:37:02] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 20:37:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-01 20:37:02] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-10-01 20:37:02] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 20:37:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 20:37:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-01 20:37:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 20:37:02] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-01 20:38:33] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 20:38:38] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 20:38:38] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 20:38:38] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 20:38:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 20:38:38] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-01 20:38:38] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 20:38:38] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-01 20:40:09] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 20:40:14] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 20:40:14] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 20:40:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 20:40:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 20:40:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-01 20:40:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 20:40:14] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-01 20:41:15] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 20:41:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 20:41:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 20:41:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 20:41:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 20:41:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 20:41:15] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 20:41:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 20:41:15] [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 0.6.37(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 3.16.2(2025-10-01); 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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); vroom 1.6.6(2025-09-19); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-10-01); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-01 20:41:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
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 504 Gateway Timeout.
--- failed re-building ‘wppi_workflow.Rmd’
SUMMARY: processing the following file failed:
‘wppi_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted