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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/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
[2025-10-09 18:03:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-09 18:03:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-09 18:03:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-09
[2025-10-09 18:03:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-09 19:05:36 UTC; unix
[2025-10-09 18:03:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-09 18:03:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-09 18:03:32] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-09; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-09 18:03:32] [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=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-09 18:03:32] [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(2025-10-09); 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 1.17.0(2025-10-09); 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)
[2025-10-09 18:03:32] [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
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-10-09 18:03:32] [INFO] [wppi] Executing WPPI workflow.
[2025-10-09 18:03:32] [INFO] [wppi] Collecting database knowledge.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-10-09 18:03:32] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:32] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-10-09 18:03:32] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-10-09 18:03:32] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-10-09 18:03:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-09 18:03:32] [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]
[2025-10-09 18:03:33] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-09 18:03:33] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.504114s from purl.obolibrary.org (2.7 Kb/s); Redirect: 0.450392s, DNS look up: 0.164735s, Connection: 0.202903s, Pretransfer: 0.233995s, First byte at: 0.503647s
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[2025-10-09 18:03:34] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-10-09 18:03:34] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:34] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-10-09 18:03:34] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 391404 records
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-10-09 18:03:34] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:34] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-10-09 18:03:34] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-10-09 18:03:34] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-10-09 18:03:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-09 18:03:34] [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]
[2025-10-09 18:03:34] [TRACE] [OmnipathR] `gz` compressed file, downloading to temporary location: `/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp3IdhJ2/goa_human.gaf.gz`
[2025-10-09 18:03:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-09 18:03:35] [TRACE] [OmnipathR] Downloaded 14.7 Mb in 0.930612s from current.geneontology.org (15.8 Mb/s); Redirect: 0s, DNS look up: 0.12131s, Connection: 0.122323s, Pretransfer: 0.122363s, First byte at: 0.741943s
[2025-10-09 18:03:35] [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: POWwsiIiATpVvDzdBktTaaekDha6BWzy8tpYyDr_ku4yv4Ukv_uEmw==; Content-Length: 15420674; Content-Type: application/gzip; Last-Modified: Fri, 25 Jul 2025 22:43:54 GMT; Date: Thu, 09 Oct 2025 04:01:21 GMT; Age: 17082; Via: 1.1 abf98c562ec8876a85f8a498028d69da.cloudfront.net (CloudFront), 1.1 phswsa6.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-10-09 18:03:40] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:40] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-10-09 18:03:40] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 993392 records
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-10-09 18:03:40] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:40] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-09 18:03:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-09 18:03:40] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-10-09 18:03:40] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-09 18:03:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-09 18:03:40] [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]
[2025-10-09 18:03:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-09 18:03:40] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-09 18:05:11] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-09 18:05:16] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-09 18:05:16] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-09 18:05:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-09 18:05:16] [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]
[2025-10-09 18:05:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-09 18:05:16] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-09 18:06:47] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-09 18:06:52] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-09 18:06:52] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-09 18:06:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-09 18:06:52] [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]
[2025-10-09 18:06:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-09 18:06:52] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-09 18:07:53] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-09 18:07:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-09 18:07:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-09
[2025-10-09 18:07:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-09 19:05:36 UTC; unix
[2025-10-09 18:07:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-09 18:07:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-09 18:07:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-09; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-09 18:07:53] [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=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-09 18:07:53] [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(2025-10-09); 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 1.17.0(2025-10-09); 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)
[2025-10-09 18:07:53] [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_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