Multiple platform build/check report for BioC 3.23 - BUILD results for OmnipathR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4868
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"	4548
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 OmnipathR on kjohnson3

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.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: OmnipathR
Version: 3.19.7
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2026-03-22 17:21:34 -0400 (Sun, 22 Mar 2026)
EndedAt: 2026-03-22 17:29:24 -0400 (Sun, 22 Mar 2026)
EllapsedTime: 469.5 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 OmnipathR
###
##############################################################################
##############################################################################


* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-22
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-22 21:21:35 UTC; unix
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-20 r89666); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-22; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-22 17:21:45] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-22 17:21:45] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2026-03-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.0(2026-03-22); 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 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.7(2026-03-22); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-22 17:21:45] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Reading JSON from `/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp7KkKQi/Rinst11a784335cb45/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Reading JSON from `/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp7KkKQi/Rinst11a784335cb45/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Reading JSON from `/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp7KkKQi/Rinst11a784335cb45/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Reading JSON from `/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp7KkKQi/Rinst11a784335cb45/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:45] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:21:46] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-22 17:21:46] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:46] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:46] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-22 17:21:46] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-22 17:21:46] [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]
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.83443s from rescued.omnipathdb.org (47.8 Kb/s); Redirect: 0s, DNS look up: 0.002395s, Connection: 0.003292s, Pretransfer: 0.552808s, First byte at: 0.695486s
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:21:46 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sun, 22 Mar 2026 22:21:46 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-22 17:21:46] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sun, 22 Mar 2026 21:21:46 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sun, 22 Mar 2026 22:21:46 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.365266s from omabrowser.org (20.7 Kb/s); Redirect: 0s, DNS look up: 0.010782s, Connection: 0.023803s, Pretransfer: 0.03997s, First byte at: 0.365026s
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sun, 22 Mar 2026 21:21:47 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=Skre3EabX2AvWnxwqqVDEvA0WaP5mgw4K3Lvup7L5IriIDGDqidcilWzlPMxyQKPdKxZH4I3wYNVaKhOS6d5t4r%2BA8RXBGwDyXgnxbVn"}]}; cf-ray: 9e083f7e1f03c96b-IAD; alt-svc: h3=":443"; ma=86400
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-22 17:21:47] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-22 17:21:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-22 17:22:01] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:01] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:01] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-22 17:22:01] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:01] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:01] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B],qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:02] [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]
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.488223s from omnipathdb.org (32.2 Kb/s); Redirect: 0s, DNS look up: 0.002365s, Connection: 0.003245s, Pretransfer: 0.328815s, First byte at: 0.488022s
[2026-03-22 17:22:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:22:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:04] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-03-22 17:22:05] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-03-22 17:22:05] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2026-03-22 17:22:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:05] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:06] [SUCCESS] [OmnipathR] Downloaded 131398 interactions.
[2026-03-22 17:22:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-03-22 17:22:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:09] [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]
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.473938s from omnipathdb.org (33.1 Kb/s); Redirect: 0s, DNS look up: 0.001465s, Connection: 0.002346s, Pretransfer: 0.314773s, First byte at: 0.473768s
[2026-03-22 17:22:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:11] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-22 17:22:11] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:11] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:11] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships.
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:12] [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]
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.311453s from omnipathdb.org (50.4 Kb/s); Redirect: 0s, DNS look up: 0.001396s, Connection: 0.002218s, Pretransfer: 0.155605s, First byte at: 0.311295s
[2026-03-22 17:22:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:14] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:22:15] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:22:15] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-03-22 17:22:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:15] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:16] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=protein complexes,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:16] [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]
[2026-03-22 17:22:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:17] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.421168s from omnipathdb.org (37.3 Kb/s); Redirect: 0s, DNS look up: 0.001079s, Connection: 0.001966s, Pretransfer: 0.190081s, First byte at: 0.421013s
[2026-03-22 17:22:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:21] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-03-22 17:22:21] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:21] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:21] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes.
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:22] [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]
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.312243s from omnipathdb.org (50.3 Kb/s); Redirect: 0s, DNS look up: 0.001602s, Connection: 0.002549s, Pretransfer: 0.154711s, First byte at: 0.312064s
[2026-03-22 17:22:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:24] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-22 17:22:24] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:24] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:24] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-22 17:22:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:25] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2026-03-22 17:22:25] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-22 17:22:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:22:26] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=HPA_tissue,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:27] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=HPA_tissue,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=DLL1,proteins2=MEIS2,proteins3=PHOX2A,proteins4=BACH1,proteins5=KLF11,proteins6=FOXO3,proteins7=MEFV],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:28] [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]
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Downloaded 16.7 Kb in 0.535365s from omnipathdb.org (31.1 Kb/s); Redirect: 0s, DNS look up: 0.001472s, Connection: 0.002226s, Pretransfer: 0.297999s, First byte at: 0.535198s
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:28] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-03-22 17:22:28] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:28] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:28] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records.
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:29] [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]
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.314752s from omnipathdb.org (49.9 Kb/s); Redirect: 0s, DNS look up: 0.00226s, Connection: 0.003357s, Pretransfer: 0.158311s, First byte at: 0.314596s
[2026-03-22 17:22:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:30] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-22 17:22:30] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:30] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:30] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:30] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:22:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:31] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-03-22 17:22:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2026-03-22 17:22:31] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-22 17:22:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:22:32] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:32] [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]
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.336571s from omnipathdb.org (46.6 Kb/s); Redirect: 0s, DNS look up: 0.001477s, Connection: 0.002464s, Pretransfer: 0.183029s, First byte at: 0.336382s
[2026-03-22 17:22:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2026-03-22 17:22:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:38] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-03-22 17:22:40] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:40] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:40] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=NA,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=NA,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.235558s from omnipathdb.org (32.2 Kb/s); Redirect: 0s, DNS look up: 0.001527s, Connection: 0.002469s, Pretransfer: 0.157949s, First byte at: 0.235446s
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:22:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:22:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:22:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:41] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-22 17:22:41] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:42] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:42] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-03-22 17:22:42] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:42] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-22 17:22:42] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-22 17:22:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:22:42] [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]
[2026-03-22 17:22:43] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-22 17:22:43] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.987491s from rest.uniprot.org (43 bytes/s); Redirect: 0s, DNS look up: 0.019561s, Connection: 0.020519s, Pretransfer: 0.659505s, First byte at: 0.987376s
[2026-03-22 17:22:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sun, 22 Mar 2026 21:22:43 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-03-22 17:22:51] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-22 17:22:51] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-03-22 17:22:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:51] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:51] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2026-03-22 17:22:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:22:53] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:53] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:22:53] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:22:55] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-03-22 17:22:55] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:55] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-03-22 17:22:55] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-22 17:22:55] [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=1,ssl_verifyhost=2]
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-22 17:22:55] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] Downloaded 346 bytes in 0.17416s from www.ensembl.org (1.9 Kb/s); Redirect: 0s, DNS look up: 0.005748s, Connection: 0.006805s, Pretransfer: 0.006845s, First byte at: 0.174098s
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Security-Policy: frame-ancestors 'self'; Date: Sun, 22 Mar 2026 21:22:55 GMT; X-Frame-Options: SAMEORIGIN; Transfer-Encoding: chunked; Content-Type: text/plain; charset=utf-8; Via: 1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] Response headers: [Server=Apache,Content-Security-Policy=frame-ancestors 'self',Date=Sun, 22 Mar 2026 21:22:55 GMT,X-Frame-Options=SAMEORIGIN,Transfer-Encoding=chunked,Content-Type=text/plain; charset=utf-8,Via=1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164),Connection=keep-alive]
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-03-22 17:22:56] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:56] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:56] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-03-22 17:22:56] [WARN]    [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2026-03-22 17:22:56] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
---
Backtrace:
     ▆
  1. ├─OmnipathR::omnipath_for_cosmos()
  2. │ └─... %T>% ...
  3. ├─dplyr::bind_rows(...)
  4. │ └─rlang::list2(...)
  5. ├─OmnipathR::translate_ids_multi(...)
  6. │ └─source_cols %>% seq_along %>% ...
  7. ├─purrr::reduce(...)
  8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
  9. │   └─OmnipathR (local) fn(out, elt, ...)
 10. │     └─OmnipathR::translate_ids(...)
 11. │       └─... %>% ...
 12. ├─purrr::reduce2(...)
 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
 14. │   └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
 15. │     ├─... %>% ...
 16. │     └─OmnipathR:::id_translation_table(...)
 17. │       └─OmnipathR::ensembl_id_mapping_table(...)
 18. │         └─... %>% trim_and_distinct
 19. ├─OmnipathR:::ensure_character(., From, To)
 20. │ └─d %>% mutate(across(c(!!!cols), as.character))
 21. ├─dplyr::mutate(., across(c(!!!cols), as.character))
 22. ├─OmnipathR:::trim_and_distinct(.)
 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 24. ├─dplyr::distinct(.)
 25. ├─dplyr::mutate(., across(everything(), str_trim))
 26. ├─rlang::set_names(., c("From", "To"))
 27. └─rlang::abort(message = message)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
The size of `nm` (2) must be compatible with the size of `x` (1).
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2026-03-22 17:22:57] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Checking on-disk cache for database `up_gs`.
[2026-03-22 17:22:57] [INFO]    [OmnipathR] Cache record does not exist: `db://up_gs`
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Loading database `up_gs` from source.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-22 17:22:57] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20431 records from cache
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Saving database `up_gs` to on-disk cache.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:57] [INFO]    [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`.
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`.
[2026-03-22 17:22:57] [INFO]    [OmnipathR] Download ready [key=7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f, version=1]
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:22:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:22:57] [INFO]    [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `started` to `ready`.
[2026-03-22 17:22:57] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:23:10] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:23:10] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:23:13] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:23:21] [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]
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.298399s from omnipathdb.org (52.6 Kb/s); Redirect: 0s, DNS look up: 0.001785s, Connection: 0.002684s, Pretransfer: 0.152727s, First byte at: 0.298226s
[2026-03-22 17:23:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:23:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:23:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:23:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-03-22 17:23:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:23:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:23:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:23:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:23:24] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:23:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-03-22 17:23:25] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-03-22 17:23:25] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2026-03-22 17:23:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:23:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:23:25] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2026-03-22 17:23:25] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-03-22 17:23:32] [SUCCESS] [OmnipathR] Downloaded 139054 interactions.
[2026-03-22 17:27:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:27:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2026-03-22 17:27:44] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_keyword,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:27:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:27:44] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:27:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_keyword,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:27:45] [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]
[2026-03-22 17:27:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:27:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.314023s from omnipathdb.org (50 Kb/s); Redirect: 0s, DNS look up: 0.001515s, Connection: 0.002381s, Pretransfer: 0.156228s, First byte at: 0.313857s
[2026-03-22 17:27:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:27:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:27:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:27:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-22 17:27:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:48] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:27:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-03-22 17:27:49] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:49] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2026-03-22 17:27:49] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records.
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=<NULL>,datasets=<NULL>,types=ubiquitination,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=<NULL>,datasets=<NULL>,types=ubiquitination,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] Downloaded 1.3 Kb in 0.235016s from omnipathdb.org (5.4 Kb/s); Redirect: 0s, DNS look up: 0.001376s, Connection: 0.002196s, Pretransfer: 0.149167s, First byte at: 0.23496s
[2026-03-22 17:27:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:27:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:27:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:27:50] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:50] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-03-22 17:27:50] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:50] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2026-03-22 17:27:50] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2026-03-22 17:27:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:27:53] [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]
[2026-03-22 17:27:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:27:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.29539s from omnipathdb.org (53.2 Kb/s); Redirect: 0s, DNS look up: 0.001418s, Connection: 0.002252s, Pretransfer: 0.146227s, First byte at: 0.295245s
[2026-03-22 17:27:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:27:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:27:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:27:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:56] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-03-22 17:27:56] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:27:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:56] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2026-03-22 17:27:57] [SUCCESS] [OmnipathR] Downloaded 67773 interactions.
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Wang,Lit-BM-17],datasets=pathwayextra,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:27:58] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Wang,Lit-BM-17],datasets=pathwayextra,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10090,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:27:59] [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=1,ssl_verifyhost=2]
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.314701s from omnipathdb.org (49.9 Kb/s); Redirect: 0s, DNS look up: 0.001383s, Connection: 0.002251s, Pretransfer: 0.155325s, First byte at: 0.314553s
[2026-03-22 17:27:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:27:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:27:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:01] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-03-22 17:28:01] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:01] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:02] [SUCCESS] [OmnipathR] Downloaded 41476 interactions.
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[PhosphoPoint,PhosphoSite],datasets=kinaseextra,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Organism(s): 10116
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[PhosphoPoint,PhosphoSite],datasets=kinaseextra,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10116,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:02] [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]
[2026-03-22 17:28:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:03] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.316611s from omnipathdb.org (49.6 Kb/s); Redirect: 0s, DNS look up: 0.001374s, Connection: 0.002205s, Pretransfer: 0.158522s, First byte at: 0.316452s
[2026-03-22 17:28:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:04] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-03-22 17:28:05] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:05] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:05] [SUCCESS] [OmnipathR] Downloaded 11083 interactions.
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[iTALK,Baccin2019],datasets=ligrecextra,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[iTALK,Baccin2019],datasets=ligrecextra,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:06] [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]
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.315387s from omnipathdb.org (49.8 Kb/s); Redirect: 0s, DNS look up: 0.001408s, Connection: 0.002127s, Pretransfer: 0.158153s, First byte at: 0.315226s
[2026-03-22 17:28:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:07] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-03-22 17:28:07] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:07] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:07] [SUCCESS] [OmnipathR] Downloaded 2840 interactions.
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:07] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:28:07] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:08] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=A,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:09] [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]
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.294888s from omnipathdb.org (53.2 Kb/s); Redirect: 0s, DNS look up: 0.00154s, Connection: 0.002428s, Pretransfer: 0.146807s, First byte at: 0.294734s
[2026-03-22 17:28:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:11] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-03-22 17:28:11] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:11] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:11] [SUCCESS] [OmnipathR] Downloaded 6128 interactions.
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[miR2Disease,miRDeathDB],datasets=mirnatarget,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[miR2Disease,miRDeathDB],datasets=mirnatarget,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:12] [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]
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Downloaded 19.1 Kb in 0.309936s from omnipathdb.org (61.6 Kb/s); Redirect: 0s, DNS look up: 0.001381s, Connection: 0.002189s, Pretransfer: 0.154555s, First byte at: 0.309747s
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:13] [SUCCESS] [OmnipathR] Downloaded 648 interactions.
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=small_molecule,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=small_molecule,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,sources=TRAMETINIB,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:13] [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]
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Downloaded 112 bytes in 0.219851s from omnipathdb.org (509 bytes/s); Redirect: 0s, DNS look up: 0.001556s, Connection: 0.002478s, Pretransfer: 0.147237s, First byte at: 0.219797s
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:14] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-03-22 17:28:14] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:14] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:14] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2026-03-22 17:28:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:15] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-22 17:28:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:16] [SUCCESS] [OmnipathR] Loaded 41506 enzyme-substrate relationships from cache.
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:16] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-22 17:28:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:17] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=[PhosphoSite,SIGNOR],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=[PhosphoSite,SIGNOR],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10090,qt_message=enzyme-substrate relationships,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:18] [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]
[2026-03-22 17:28:19] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:19] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.315917s from omnipathdb.org (49.7 Kb/s); Redirect: 0s, DNS look up: 0.001505s, Connection: 0.002362s, Pretransfer: 0.159387s, First byte at: 0.315759s
[2026-03-22 17:28:19] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:20] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-03-22 17:28:20] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:20] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:20] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships.
[2026-03-22 17:28:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,organism=9606,resources=[CORUM,hu.MAP],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,resources=[CORUM,hu.MAP],datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=protein complexes,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:22] [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]
[2026-03-22 17:28:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.595613s from omnipathdb.org (26.4 Kb/s); Redirect: 0s, DNS look up: 0.001569s, Connection: 0.002368s, Pretransfer: 0.263652s, First byte at: 0.595465s
[2026-03-22 17:28:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:25] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-03-22 17:28:25] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:25] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:25] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes.
[2026-03-22 17:28:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,proteins2=COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,proteins3=COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,proteins4=COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,proteins5=COMPLEX:TERF2_WRN,proteins6=COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,proteins7=COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,proteins8=COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,proteins9=COMPLEX:CDK8_MED6_PARP1,proteins10=COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:29] [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]
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Downloaded 11.6 Kb in 0.292219s from omnipathdb.org (39.8 Kb/s); Redirect: 0s, DNS look up: 0.001599s, Connection: 0.002714s, Pretransfer: 0.148582s, First byte at: 0.292081s
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:30] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-03-22 17:28:30] [INFO]    [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1]
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:30] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:30] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records.
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=NetPath,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=NetPath,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=NCAPD2,proteins2=NCAPG,proteins3=NCAPH,proteins4=PARP1,proteins5=SMC2,proteins6=SMC4,proteins7=XRCC1,proteins8=CCNA2,proteins9=CDK2,proteins10=LIG1,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:30] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:30] [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]
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Downloaded 1.2 Kb in 0.232524s from omnipathdb.org (5.2 Kb/s); Redirect: 0s, DNS look up: 0.001579s, Connection: 0.002435s, Pretransfer: 0.155603s, First byte at: 0.232475s
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:31] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-03-22 17:28:31] [INFO]    [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1]
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:31] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:31] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=ComPPI,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=ComPPI,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=NCAPD2,proteins2=NCAPG,proteins3=NCAPH,proteins4=PARP1,proteins5=SMC2,proteins6=SMC4,proteins7=XRCC1,proteins8=CCNA2,proteins9=CDK2,proteins10=LIG1,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:32] [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]
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Downloaded 2.7 Kb in 0.230667s from omnipathdb.org (11.8 Kb/s); Redirect: 0s, DNS look up: 0.001426s, Connection: 0.002165s, Pretransfer: 0.153625s, First byte at: 0.230601s
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:33] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-03-22 17:28:33] [INFO]    [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1]
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:33] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:33] [SUCCESS] [OmnipathR] Downloaded 366 annotation records.
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:28:33] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-22 17:28:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-22 17:28:33] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=NA,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=NA,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-22 17:28:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2026-03-22 17:28:34] [SUCCESS] [OmnipathR] Loaded 1190 records from cache.
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=generic,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=generic,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:34] [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]
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.295348s from omnipathdb.org (53.2 Kb/s); Redirect: 0s, DNS look up: 0.001668s, Connection: 0.002544s, Pretransfer: 0.146923s, First byte at: 0.295166s
[2026-03-22 17:28:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-22 17:28:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:38] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-03-22 17:28:39] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:39] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:39] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records.
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2026-03-22 17:28:39] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2026-03-22 17:28:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2026-03-22 17:28:40] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=TFcensus,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:40] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=TFcensus,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.310298s from omnipathdb.org (50.6 Kb/s); Redirect: 0s, DNS look up: 0.001368s, Connection: 0.002173s, Pretransfer: 0.155143s, First byte at: 0.310121s
[2026-03-22 17:28:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:42] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:42] [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]
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Downloaded 2.7 Kb in 0.090888s from static-content.springer.com (29.5 Kb/s); Redirect: 0s, DNS look up: 0.004137s, Connection: 0.00511s, Pretransfer: 0.071716s, First byte at: 0.090428s
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AGQBYWzdIlLrpj35oTGayVLa7k3forGrIWDNir9VrNGruogB9A-ULs3ek_VwNGiLC1BxqaLN47rleNw; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 59479; date: Sun, 22 Mar 2026 21:28:42 GMT; via: 1.1 varnish; x-served-by: cache-iad-kcgs7200120-IAD; x-cache: HIT; x-cache-hits: 0; x-timer: S1774214922.492651,VS0,VE3; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-03-22 17:28:42] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:43] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:43] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C],entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:43] [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]
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.297794s from omnipathdb.org (52.7 Kb/s); Redirect: 0s, DNS look up: 0.001478s, Connection: 0.00228s, Pretransfer: 0.149369s, First byte at: 0.297594s
[2026-03-22 17:28:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-22 17:28:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:45] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-03-22 17:28:46] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-03-22 17:28:46] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2026-03-22 17:28:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:46] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:48] [SUCCESS] [OmnipathR] Downloaded 147217 interactions.
[2026-03-22 17:28:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:28:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2026-03-22 17:28:48] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:48] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.364759s from omnipathdb.org (43 Kb/s); Redirect: 0s, DNS look up: 0.001601s, Connection: 0.002478s, Pretransfer: 0.170634s, First byte at: 0.364598s
[2026-03-22 17:28:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:53] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-22 17:28:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:53] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-03-22 17:28:54] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:54] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:54] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records.
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=ligand,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=<NULL>,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=ligand,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=<NULL>,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:54] [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]
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.319846s from omnipathdb.org (49.1 Kb/s); Redirect: 0s, DNS look up: 0.001436s, Connection: 0.002375s, Pretransfer: 0.160823s, First byte at: 0.319654s
[2026-03-22 17:28:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:55] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-03-22 17:28:55] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:55] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:56] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records.
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:56] [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]
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.294595s from omnipathdb.org (53.3 Kb/s); Redirect: 0s, DNS look up: 0.001449s, Connection: 0.002396s, Pretransfer: 0.148178s, First byte at: 0.29442s
[2026-03-22 17:28:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:57] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records.
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=receptor,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=<NULL>,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=receptor,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=<NULL>,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-22 17:28:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:28:58] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.453258s from omnipathdb.org (34.6 Kb/s); Redirect: 0s, DNS look up: 0.001491s, Connection: 0.0025s, Pretransfer: 0.216617s, First byte at: 0.45307s
[2026-03-22 17:28:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:28:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:28:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2026-03-22 17:28:59] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records.
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:28:59] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=trans,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=trans,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:28:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:28:59] [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=1,ssl_verifyhost=2]
[2026-03-22 17:29:00] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:00] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.297152s from omnipathdb.org (52.8 Kb/s); Redirect: 0s, DNS look up: 0.001453s, Connection: 0.002449s, Pretransfer: 0.146692s, First byte at: 0.29699s
[2026-03-22 17:29:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:01] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records.
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:29:01] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=rec,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=rec,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:29:01] [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]
[2026-03-22 17:29:02] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:02] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.318257s from omnipathdb.org (49.3 Kb/s); Redirect: 0s, DNS look up: 0.002185s, Connection: 0.003067s, Pretransfer: 0.154527s, First byte at: 0.318064s
[2026-03-22 17:29:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:03] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records.
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-22 17:29:03] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:03] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:29:03] [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]
[2026-03-22 17:29:04] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:04] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.301925s from omnipathdb.org (52 Kb/s); Redirect: 0s, DNS look up: 0.001417s, Connection: 0.002394s, Pretransfer: 0.148983s, First byte at: 0.301755s
[2026-03-22 17:29:04] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:06] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-03-22 17:29:06] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:06] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:08] [SUCCESS] [OmnipathR] Downloaded 84507 interactions.
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:29:08] [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]
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Downloaded 11.4 Kb in 0.295027s from omnipathdb.org (38.7 Kb/s); Redirect: 0s, DNS look up: 0.001436s, Connection: 0.002249s, Pretransfer: 0.155412s, First byte at: 0.294886s
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:09] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-03-22 17:29:09] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:09] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:09] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records.
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_function,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_function,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:29:10] [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]
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] Downloaded 10.6 Kb in 0.269488s from omnipathdb.org (39.3 Kb/s); Redirect: 0s, DNS look up: 0.001579s, Connection: 0.002333s, Pretransfer: 0.137749s, First byte at: 0.269363s
[2026-03-22 17:29:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:11] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-03-22 17:29:11] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:11] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:11] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records.
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[ORegAnno,PAZAR],datasets=tf_target,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[ORegAnno,PAZAR],datasets=tf_target,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B],entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:29:13] [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]
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.299978s from omnipathdb.org (52.3 Kb/s); Redirect: 0s, DNS look up: 0.001297s, Connection: 0.002018s, Pretransfer: 0.148771s, First byte at: 0.299805s
[2026-03-22 17:29:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:14] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-03-22 17:29:14] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:14] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:14] [SUCCESS] [OmnipathR] Downloaded 4242 interactions.
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-22 17:29:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:29:15] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=kinase.com,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=kinase.com,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-22 17:29:16] [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]
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] Downloaded 17.1 Kb in 0.27538s from omnipathdb.org (62.1 Kb/s); Redirect: 0s, DNS look up: 0.001501s, Connection: 0.002499s, Pretransfer: 0.137308s, First byte at: 0.275184s
[2026-03-22 17:29:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Mar 2026 21:29:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 22 Mar 2026 22:29:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-22 17:29:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:17] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-03-22 17:29:17] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-22 17:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:17] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2026-03-22 17:29:17] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records.
[2026-03-22 17:29:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-03-22 17:29:20] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-22 17:29:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-22 17:29:21] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-03-22 17:29:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=kinase.com,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=kinase.com,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:22] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-03-22 17:29:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-22 17:29:22] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache.
--- finished re-building ‘paths.Rmd’

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

Error: Vignette re-building failed.
Execution halted