Multiple platform build/check report for BioC 3.22 - BUILD results for OmnipathR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 lconway

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: 3.17.6
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2025-10-23 18:00:37 -0400 (Thu, 23 Oct 2025)
EndedAt: 2025-10-23 18:20:53 -0400 (Thu, 23 Oct 2025)
EllapsedTime: 1216.2 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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2025-10-23 18:01:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-23
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-23 22:00:39 UTC; unix
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-23; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-23 18:01:05] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-23 18:01:05] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-10-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-23); 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 1.4.0(2025-10-22); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-23 18:01:05] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-23 18:01:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-23 18:01:05] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp85ZECN/Rinst176d137b1bc2d/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp85ZECN/Rinst176d137b1bc2d/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp85ZECN/Rinst176d137b1bc2d/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/Rtmp85ZECN/Rinst176d137b1bc2d/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-10-23 18:01:06] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:06] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-10-23 18:01:06] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-23 18:01:06] [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]
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-23 18:01:06] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Downloaded 31.3 Kb in 8.989788s from www.ensembl.org (3.5 Kb/s); Redirect: 8.757786s, DNS look up: 0.004554s, Connection: 0.006306s, Pretransfer: 0.698554s, First byte at: 8.958149s
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Thu, 23 Oct 2025 22:01:06 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk; HTTP/2 302 ; date: Thu, 23 Oct 2025 22:01:15 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-94.us-east-2.compute.internal; HTTP/2 200 ; date: Thu, 23 Oct 2025 22:01:15 GMT; content-type: text/html; charset=utf-8; content-length: 32009; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Fri, 24 Oct 2025 21:57:41 GMT; set-cookie: ENSEMBL_WWW_SESSION=501b1cad4b84ae760bdc73c66949bed604c1dfaefcc70f252fe04135; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Fri, 24 Oct 2025 21:57:41 GMT; set-cookie: ENSEMBL_WWW_SESSION=501b1cad4b84ae760bdc73c66949bed604c1dfaefcc70f252fe04135; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-68.us-east-2.compute.internal
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Response headers: [date=Thu, 23 Oct 2025 22:01:15 GMT,content-type=text/html; charset=utf-8,content-length=32009,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Fri, 24 Oct 2025 21:57:41 GMT,set-cookie=ENSEMBL_WWW_SESSION=501b1cad4b84ae760bdc73c66949bed604c1dfaefcc70f252fe04135; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Fri, 24 Oct 2025 21:57:41 GMT,set-cookie=ENSEMBL_WWW_SESSION=501b1cad4b84ae760bdc73c66949bed604c1dfaefcc70f252fe04135; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-68.us-east-2.compute.internal]
[2025-10-23 18:01:15] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:15] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-10-23 18:01:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:15] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-10-23 18:01:15] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:01:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:01:16] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-10-23 18:01:16] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.847817s from omabrowser.org (10.2 Kb/s); Redirect: 0s, DNS look up: 0.305697s, Connection: 0.306612s, Pretransfer: 0.76285s, First byte at: 0.847571s
[2025-10-23 18:01:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 23 Oct 2025 22:01:16 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-10-23 18:01:17] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-10-23 18:01:17] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:17] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-10-23 18:01:17] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-10-23 18:01:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-10-23 18:01:52] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-10-23 18:01:52] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-10-23 18:01:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:01:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:01:52] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-10-23 18:01:53] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-10-23 18:01:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:01:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [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`
[2025-10-23 18:01:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:01:53] [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]
[2025-10-23 18:01:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:01:59] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 6.719538s from omnipathdb.org (2.3 Kb/s); Redirect: 0s, DNS look up: 6.262809s, Connection: 6.26373s, Pretransfer: 6.571946s, First byte at: 6.718927s
[2025-10-23 18:01:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:01:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:01:59 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:02] [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`
[2025-10-23 18:02:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:02] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-10-23 18:02:03] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-10-23 18:02:03] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-10-23 18:02:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:03] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:09] [SUCCESS] [OmnipathR] Downloaded 131398 interactions.
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.295641s from omnipathdb.org (53 Kb/s); Redirect: 0s, DNS look up: 0.001105s, Connection: 0.00221s, Pretransfer: 0.149116s, First byte at: 0.294803s
[2025-10-23 18:02:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:17] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-10-23 18:02:17] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:17] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:19] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships.
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:21] [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`
[2025-10-23 18:02:21] [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`
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:21] [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]
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.309246s from omnipathdb.org (50.7 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.001905s, Pretransfer: 0.157912s, First byte at: 0.308869s
[2025-10-23 18:02:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:24] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:02:25] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:02:25] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-10-23 18:02:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:25] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:28] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:29] [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]
[2025-10-23 18:02:30] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:30] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.473582s from omnipathdb.org (33.1 Kb/s); Redirect: 0s, DNS look up: 0.001245s, Connection: 0.002358s, Pretransfer: 0.33883s, First byte at: 0.473308s
[2025-10-23 18:02:30] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:30 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-10-23 18:02:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:32] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-10-23 18:02:33] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:33] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:33] [SUCCESS] [OmnipathR] Downloaded 52085 protein complexes.
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:02:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:34] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.291827s from omnipathdb.org (53.7 Kb/s); Redirect: 0s, DNS look up: 0.001022s, Connection: 0.001983s, Pretransfer: 0.146841s, First byte at: 0.29146s
[2025-10-23 18:02:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:34 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:36] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-10-23 18:02:36] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:36] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:36] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.361994s from omnipathdb.org (165 bytes/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.001928s, Pretransfer: 0.294767s, First byte at: 0.361937s
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:38 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:38 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-10-23 18:02:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:38] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-10-23 18:02:38] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:38] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:38] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-10-23 18:02:38] [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.
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:02:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:39] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-10-23 18:02:39] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:02:39] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-10-23 18:02:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-10-23 18:02:40] [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`
[2025-10-23 18:02:40] [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`
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-10-23 18:02:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.293586s from omnipathdb.org (53.4 Kb/s); Redirect: 0s, DNS look up: 0.001104s, Connection: 0.002144s, Pretransfer: 0.148463s, First byte at: 0.293194s
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:41] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-10-23 18:02:41] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:41] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:41] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records.
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:42] [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]
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.308347s from omnipathdb.org (50.8 Kb/s); Redirect: 0s, DNS look up: 0.001279s, Connection: 0.002101s, Pretransfer: 0.155178s, First byte at: 0.30802s
[2025-10-23 18:02:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:43] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-10-23 18:02:43] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:43] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-10-23 18:02:43] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:44] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:02:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:02:48] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2025-10-23 18:02:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:02:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-10-23 18:02:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-10-23 18:02:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-10-23 18:02:49] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:02:49] [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]
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.290498s from omnipathdb.org (53.9 Kb/s); Redirect: 0s, DNS look up: 0.001152s, Connection: 0.002234s, Pretransfer: 0.147732s, First byte at: 0.290044s
[2025-10-23 18:02:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:02:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:02:49 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:02:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-10-23 18:02:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:02:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:02:56] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:02:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-10-23 18:03:00] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-10-23 18:03:00] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-10-23 18:03:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:00] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-10-23 18:03:01] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records.
[2025-10-23 18:03:04] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-10-23 18:03:04] [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.
[2025-10-23 18:03:04] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-10-23 18:03:04] [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.
[2025-10-23 18:03:04] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-10-23 18:03:04] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-10-23 18:03:04] [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.
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:03:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:03:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:03:06] [TRACE]   [OmnipathR] Downloaded 9.4 Kb in 0.222796s from omnipathdb.org (42.1 Kb/s); Redirect: 0s, DNS look up: 0.0012s, Connection: 0.002292s, Pretransfer: 0.148931s, First byte at: 0.22249s
[2025-10-23 18:03:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:03:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:03:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:03:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:07] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-10-23 18:03:07] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:07] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-10-23 18:03:07] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:03:07] [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`.
[2025-10-23 18:03:07] [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`
[2025-10-23 18:03:07] [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`.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:07] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-10-23 18:03:07] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:03:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:03:11] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-10-23 18:03:11] [TRACE]   [OmnipathR] Downloaded 43 bytes in 3.8762s from rest.uniprot.org (11 bytes/s); Redirect: 0s, DNS look up: 3.042996s, Connection: 3.04439s, Pretransfer: 3.54535s, First byte at: 3.876042s
[2025-10-23 18:03:11] [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: 15-October-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 23 Oct 2025 22:03:11 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; 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: 15-October-2025
[2025-10-23 18:03:22] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-10-23 18:03:22] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-10-23 18:03:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:22] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-10-23 18:03:22] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-10-23 18:03:23] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-10-23 18:03:23] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-10-23 18:03:23] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-10-23 18:03:23] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-10-23 18:03:23] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-10-23 18:03:24] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-10-23 18:03:24] [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.
[2025-10-23 18:03:24] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-10-23 18:03:24] [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.
[2025-10-23 18:03:24] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-10-23 18:03:24] [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
[2025-10-23 18:03:28] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-10-23 18:03:28] [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.
[2025-10-23 18:03:28] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-10-23 18:03:28] [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.
[2025-10-23 18:03:29] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-10-23 18:03:29] [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.
[2025-10-23 18:03:29] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-10-23 18:03:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:03:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-10-23 18:03:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:03:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:03:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:03:30] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:03:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:03:34] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2025-10-23 18:03:34] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-10-23 18:03:34] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-10-23 18:03:34] [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>
[2025-10-23 18:03:34] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:03:34] [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`.
[2025-10-23 18:03:34] [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`
[2025-10-23 18:03:35] [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`.
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:03:35] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-10-23 18:03:35] [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`
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-23 18:03:35] [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`
[2025-10-23 18:03:35] [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`.
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-23 18:03:35] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-23 18:04:05] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-10-23 18:04:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:04:05] [TRACE]   [OmnipathR] Downloaded 2 Mb in 30.260172s from www.ensembl.org (67.7 Kb/s); Redirect: 0s, DNS look up: 0.002343s, Connection: 0.003175s, Pretransfer: 0.003264s, First byte at: 2.193267s
[2025-10-23 18:04:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Security-Policy: frame-ancestors 'self'; Date: Thu, 23 Oct 2025 22:03:35 GMT; X-Frame-Options: SAMEORIGIN; Transfer-Encoding: chunked; Content-Type: text/plain; charset=utf-8; Via: 1.1 phswsa23.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2025-10-23 18:04:05] [TRACE]   [OmnipathR] Response headers: [Server=Apache,Content-Security-Policy=frame-ancestors 'self',Date=Thu, 23 Oct 2025 22:03:35 GMT,X-Frame-Options=SAMEORIGIN,Transfer-Encoding=chunked,Content-Type=text/plain; charset=utf-8,Via=1.1 phswsa23.partners.org:80 (Cisco-WSA/15.0.1-004),Connection=keep-alive]
[2025-10-23 18:04:05] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-10-23 18:04:07] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-10-23 18:04:07] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-10-23 18:04:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:04:08] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-10-23 18:04:08] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 244093 records
[2025-10-23 18:04:08] [TRACE]   [OmnipathR] Translating complexes: 612 complexes in data.
[2025-10-23 18:04:08] [TRACE]   [OmnipathR] 451 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] Translated 451 complexes to 451.
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] 71139 rows before translation, 4827 uniprot IDs in column `source`.
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] 71220 rows after translation; translated 4827 `uniprot` IDs in column `source` to 4663 `genesymbol` IDs in column `genesymbol_source`.
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-10-23 18:04:10] [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>
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:04:10] [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`.
[2025-10-23 18:04:10] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-10-23 18:04:10] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 244093 records from cache
[2025-10-23 18:04:11] [TRACE]   [OmnipathR] Translating complexes: 381 complexes in data.
[2025-10-23 18:04:11] [TRACE]   [OmnipathR] 229 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-10-23 18:04:12] [TRACE]   [OmnipathR] Translated 229 complexes to 229.
[2025-10-23 18:04:12] [TRACE]   [OmnipathR] 71220 rows before translation, 5240 uniprot IDs in column `target`.
[2025-10-23 18:04:12] [TRACE]   [OmnipathR] 72796 rows after translation; translated 5240 `uniprot` IDs in column `target` to 5086 `genesymbol` IDs in column `genesymbol_target`.
[2025-10-23 18:04:12] [INFO]    [OmnipathR] OmniPath PPI for COSMOS PKN ready: 145749 interactions.
--- finished re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2025-10-23 18:04:16] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-10-23 18:04:16] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-10-23 18:04:16] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-10-23 18:04:16] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:04:16] [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`.
[2025-10-23 18:04:16] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-10-23 18:04:16] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20420 records from cache
[2025-10-23 18:04:18] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:04:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:04:36] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:04:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:04:44] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
2025-10-23 18:04:54.936 R[98462:624617340] XType: com.apple.fonts is not accessible.
2025-10-23 18:04:54.937 R[98462:624617340] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-10-23 18:05:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:05:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-10-23 18:05:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:05:02] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [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`
[2025-10-23 18:05:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:05:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:05:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:05:03] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.440564s from omnipathdb.org (35.6 Kb/s); Redirect: 0s, DNS look up: 0.001676s, Connection: 0.002789s, Pretransfer: 0.294133s, First byte at: 0.440009s
[2025-10-23 18:05:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:05:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:05:03 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:05:09] [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`
[2025-10-23 18:05:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:05:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:05:09] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:05:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-10-23 18:05:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-10-23 18:05:11] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-10-23 18:05:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:05:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:05:11] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-10-23 18:05:11] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-10-23 18:05:35] [SUCCESS] [OmnipathR] Downloaded 139054 interactions.
[2025-10-23 18:18:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:18:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-10-23 18:18:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:18:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:18:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.447167s from omnipathdb.org (35 Kb/s); Redirect: 0s, DNS look up: 0.001119s, Connection: 0.002008s, Pretransfer: 0.302031s, First byte at: 0.446605s
[2025-10-23 18:18:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:18:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:18:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:18:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-10-23 18:18:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:43] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:18:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-10-23 18:18:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-10-23 18:18:44] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-10-23 18:18:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:44] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-10-23 18:18:44] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records.
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-10-23 18:18:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-10-23 18:18:45] [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`
[2025-10-23 18:18:45] [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`
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-10-23 18:18:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:18:45] [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]
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] Downloaded 11.6 Kb in 0.430542s from omnipathdb.org (27 Kb/s); Redirect: 0s, DNS look up: 0.001521s, Connection: 0.002775s, Pretransfer: 0.290644s, First byte at: 0.430483s
[2025-10-23 18:18:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:18:45 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 11882; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:18:45 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-10-23 18:18:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:46] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-10-23 18:18:46] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:46] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-10-23 18:18:46] [SUCCESS] [OmnipathR] Downloaded 164 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
[2025-10-23 18:18:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:18:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:53] [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`
[2025-10-23 18:18:53] [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`
[2025-10-23 18:18:53] [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`
[2025-10-23 18:18:53] [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`
[2025-10-23 18:18:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:18:54] [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`
[2025-10-23 18:18:54] [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`
[2025-10-23 18:18:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:18:54] [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]
[2025-10-23 18:18:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:18:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.30765s from omnipathdb.org (50.9 Kb/s); Redirect: 0s, DNS look up: 0.001057s, Connection: 0.001869s, Pretransfer: 0.155102s, First byte at: 0.30722s
[2025-10-23 18:18:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:18:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:18:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:18:57] [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`
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:57] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-10-23 18:18:57] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:18:57] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:00] [SUCCESS] [OmnipathR] Downloaded 67773 interactions.
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [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`
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:05] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.310315s from omnipathdb.org (50.5 Kb/s); Redirect: 0s, DNS look up: 0.001107s, Connection: 0.002043s, Pretransfer: 0.157023s, First byte at: 0.309974s
[2025-10-23 18:19:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:07] [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`
[2025-10-23 18:19:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:07] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-10-23 18:19:08] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-10-23 18:19:08] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-10-23 18:19:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:08] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:10] [SUCCESS] [OmnipathR] Downloaded 41476 interactions.
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:11] [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`
[2025-10-23 18:19:11] [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`
[2025-10-23 18:19:11] [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`
[2025-10-23 18:19:11] [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`
[2025-10-23 18:19:11] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:11] [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`
[2025-10-23 18:19:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:11] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:11] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:11] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.289431s from omnipathdb.org (54.1 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.001955s, Pretransfer: 0.14559s, First byte at: 0.289057s
[2025-10-23 18:19:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:11 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:13] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-10-23 18:19:13] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:13] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:14] [SUCCESS] [OmnipathR] Downloaded 11083 interactions.
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:15] [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`
[2025-10-23 18:19:15] [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`
[2025-10-23 18:19:15] [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`
[2025-10-23 18:19:15] [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`
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:15] [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`
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.310511s from omnipathdb.org (50.5 Kb/s); Redirect: 0s, DNS look up: 0.001271s, Connection: 0.002438s, Pretransfer: 0.157596s, First byte at: 0.310168s
[2025-10-23 18:19:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:16] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-10-23 18:19:16] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:16] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:17] [SUCCESS] [OmnipathR] Downloaded 2840 interactions.
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:17] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:19:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:21] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2025-10-23 18:19:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-10-23 18:19:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [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`
[2025-10-23 18:19:23] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:24] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.30936s from omnipathdb.org (50.6 Kb/s); Redirect: 0s, DNS look up: 0.000909s, Connection: 0.001756s, Pretransfer: 0.154899s, First byte at: 0.309069s
[2025-10-23 18:19:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:24 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:25] [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`
[2025-10-23 18:19:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:25] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-10-23 18:19:26] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:26] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:26] [SUCCESS] [OmnipathR] Downloaded 6128 interactions.
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:27] [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`
[2025-10-23 18:19:27] [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`
[2025-10-23 18:19:27] [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`
[2025-10-23 18:19:27] [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`
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:27] [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`
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.273182s from omnipathdb.org (57.3 Kb/s); Redirect: 0s, DNS look up: 0.001094s, Connection: 0.001987s, Pretransfer: 0.138118s, First byte at: 0.272291s
[2025-10-23 18:19:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:27 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:28] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-10-23 18:19:28] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:28] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:28] [SUCCESS] [OmnipathR] Downloaded 648 interactions.
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-10-23 18:19:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:29] [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`
[2025-10-23 18:19:29] [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`
[2025-10-23 18:19:29] [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`
[2025-10-23 18:19:29] [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`
[2025-10-23 18:19:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-10-23 18:19:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-10-23 18:19:29] [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`
[2025-10-23 18:19:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:29] [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]
[2025-10-23 18:19:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:29] [TRACE]   [OmnipathR] Downloaded 189 bytes in 0.219178s from omnipathdb.org (862 bytes/s); Redirect: 0s, DNS look up: 0.001134s, Connection: 0.002072s, Pretransfer: 0.147727s, First byte at: 0.219104s
[2025-10-23 18:19:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:29 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 189; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:29 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-10-23 18:19:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:30] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-10-23 18:19:30] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:30] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:30] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-10-23 18:19:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:31] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:31] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-10-23 18:19:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:33] [SUCCESS] [OmnipathR] Loaded 47840 enzyme-substrate relationships from cache.
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:33] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-10-23 18:19:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:37] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2025-10-23 18:19:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-10-23 18:19:39] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-10-23 18:19:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:40] [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`
[2025-10-23 18:19:40] [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`
[2025-10-23 18:19:40] [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`
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.308842s from omnipathdb.org (50.7 Kb/s); Redirect: 0s, DNS look up: 0.001177s, Connection: 0.002083s, Pretransfer: 0.155556s, First byte at: 0.308402s
[2025-10-23 18:19:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:42] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-10-23 18:19:42] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-10-23 18:19:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:43] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:44] [SUCCESS] [OmnipathR] Downloaded 19838 enzyme-substrate relationships.
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:45] [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]
[2025-10-23 18:19:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.309432s from omnipathdb.org (50.6 Kb/s); Redirect: 0s, DNS look up: 0.001228s, Connection: 0.002313s, Pretransfer: 0.15628s, First byte at: 0.30903s
[2025-10-23 18:19:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:47] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-10-23 18:19:47] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:47] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:48] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes.

Quitting from omnipath_intro.Rmd:593-611 [enrichment]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gprofiler_request()`:
! There's an issue with your request to g:Profiler.
Error code: 503.
Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
---
Backtrace:
    ▆
 1. └─gprofiler2::gost(...)
 2.   └─gprofiler2::get_version_info(organism = organism)
 3.     └─gprofiler2:::gprofiler_request(url, body)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
There's an issue with your request to g:Profiler.
Error code: 503.
Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2025-10-23 18:19:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-10-23 18:19:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:51] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.293528s from omnipathdb.org (53.4 Kb/s); Redirect: 0s, DNS look up: 0.001142s, Connection: 0.002229s, Pretransfer: 0.14941s, First byte at: 0.293144s
[2025-10-23 18:19:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:51] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-10-23 18:19:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:52] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-10-23 18:19:52] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:52] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:52] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-10-23 18:19:52] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-10-23 18:19:52] [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`.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:52] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-10-23 18:19:52] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] Downloaded 9.4 Kb in 0.079799s from static-content.springer.com (117.9 Kb/s); Redirect: 0s, DNS look up: 0.004683s, Connection: 0.005575s, Pretransfer: 0.06296s, First byte at: 0.079063s
[2025-10-23 18:19:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AAwnv3L8GyGzxDLB4nDARzLMYdEgaOHQZoFMRM4_RshTxP2Xwt4JWbM91Go0zTv9NKsLfoHiNSyNfYE; 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: 3249; date: Thu, 23 Oct 2025 22:19:52 GMT; via: 1.1 varnish; x-served-by: cache-iad-kcgs7200174-IAD; x-cache: HIT; x-cache-hits: 0; x-timer: S1761257993.788136,VS0,VE3; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2025-10-23 18:19:53] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-10-23 18:19:53] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-10-23 18:19:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:53] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-10-23 18:19:53] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-10-23 18:19:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:19:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-10-23 18:19:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:19:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [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`
[2025-10-23 18:19:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:19:54] [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]
[2025-10-23 18:19:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:19:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.291679s from omnipathdb.org (53.7 Kb/s); Redirect: 0s, DNS look up: 0.0011s, Connection: 0.002115s, Pretransfer: 0.146956s, First byte at: 0.291335s
[2025-10-23 18:19:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:19:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:19:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:19:57] [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`
[2025-10-23 18:19:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:57] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:19:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-10-23 18:19:58] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-10-23 18:19:58] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-10-23 18:19:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:19:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:19:58] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:03] [SUCCESS] [OmnipathR] Downloaded 124225 interactions.
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:04] [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`
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:05] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.2958s from omnipathdb.org (53 Kb/s); Redirect: 0s, DNS look up: 0.00133s, Connection: 0.002267s, Pretransfer: 0.14914s, First byte at: 0.295202s
[2025-10-23 18:20:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-10-23 18:20:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:09] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-10-23 18:20:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-10-23 18:20:11] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-10-23 18:20:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:11] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:11] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records.
[2025-10-23 18:20:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:13] [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]
[2025-10-23 18:20:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:13] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.309255s from omnipathdb.org (50.7 Kb/s); Redirect: 0s, DNS look up: 0.001184s, Connection: 0.002271s, Pretransfer: 0.156921s, First byte at: 0.308799s
[2025-10-23 18:20:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:14] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-10-23 18:20:14] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:14] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:14] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records.
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:15] [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`
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.290934s from omnipathdb.org (53.9 Kb/s); Redirect: 0s, DNS look up: 0.001003s, Connection: 0.001872s, Pretransfer: 0.147776s, First byte at: 0.290441s
[2025-10-23 18:20:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:17] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-10-23 18:20:17] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:17] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:17] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records.
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.307594s from omnipathdb.org (50.9 Kb/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.002043s, Pretransfer: 0.155462s, First byte at: 0.307137s
[2025-10-23 18:20:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:19] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-10-23 18:20:19] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:19] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:19] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records.
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:19] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-10-23 18:20:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:20] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.308405s from omnipathdb.org (50.8 Kb/s); Redirect: 0s, DNS look up: 0.00098s, Connection: 0.002015s, Pretransfer: 0.156578s, First byte at: 0.308045s
[2025-10-23 18:20:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:20 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:22] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records.
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:22] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:22] [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]
[2025-10-23 18:20:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.290401s from omnipathdb.org (53.9 Kb/s); Redirect: 0s, DNS look up: 0.001099s, Connection: 0.002008s, Pretransfer: 0.147301s, First byte at: 0.290066s
[2025-10-23 18:20:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:23 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-10-23 18:20:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:24] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-10-23 18:20:25] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:25] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:25] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records.
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-10-23 18:20:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-10-23 18:20:25] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:25] [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`
[2025-10-23 18:20:25] [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`
[2025-10-23 18:20:25] [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`
[2025-10-23 18:20:25] [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`
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-10-23 18:20:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-10-23 18:20:25] [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`
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:25] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.306029s from omnipathdb.org (51.2 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.001913s, Pretransfer: 0.155036s, First byte at: 0.30562s
[2025-10-23 18:20:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-10-23 18:20:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:28] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-10-23 18:20:29] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-10-23 18:20:29] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-10-23 18:20:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:29] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:31] [SUCCESS] [OmnipathR] Downloaded 32281 interactions.
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:32] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.306047s from omnipathdb.org (42.8 Kb/s); Redirect: 0s, DNS look up: 0.001128s, Connection: 0.002109s, Pretransfer: 0.155875s, First byte at: 0.30577s
[2025-10-23 18:20:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:33] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-10-23 18:20:33] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:33] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:33] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records.
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] Downloaded 12.2 Kb in 0.305726s from omnipathdb.org (39.8 Kb/s); Redirect: 0s, DNS look up: 0.001101s, Connection: 0.002228s, Pretransfer: 0.15577s, First byte at: 0.30542s
[2025-10-23 18:20:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:34 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:35] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-10-23 18:20:35] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:35] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:35] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records.
[2025-10-23 18:20:37] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-10-23 18:20:37] [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.
[2025-10-23 18:20:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-10-23 18:20:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [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`
[2025-10-23 18:20:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-23 18:20:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:38] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.307219s from omnipathdb.org (51 Kb/s); Redirect: 0s, DNS look up: 0.001204s, Connection: 0.002035s, Pretransfer: 0.155795s, First byte at: 0.306785s
[2025-10-23 18:20:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:38 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:39] [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`
[2025-10-23 18:20:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:40] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-10-23 18:20:40] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:40] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:40] [SUCCESS] [OmnipathR] Downloaded 4242 interactions.
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:20:41] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-10-23 18:20:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:20:41] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-23 18:20:42] [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]
[2025-10-23 18:20:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-10-23 18:20:43] [TRACE]   [OmnipathR] Downloaded 21.1 Kb in 0.440487s from omnipathdb.org (47.9 Kb/s); Redirect: 0s, DNS look up: 0.00115s, Connection: 0.002084s, Pretransfer: 0.298666s, First byte at: 0.43995s
[2025-10-23 18:20:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 23 Oct 2025 22:20:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 23 Oct 2025 23:20:43 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-23 18:20:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:44] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-10-23 18:20:44] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-23 18:20:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:44] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-10-23 18:20:44] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records.
[2025-10-23 18:20:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-10-23 18:20:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:20:48] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-10-23 18:20:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-10-23 18:20:48] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:49] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-10-23 18:20:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-10-23 18:20:49] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache.
--- finished re-building ‘paths.Rmd’

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

Error: Vignette re-building failed.
Execution halted